Bottom Line:
The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species.We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes.We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

Affiliation: Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan. hnishida@iu.a.u-tokyo.ac.jp

ABSTRACTWe present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nucleosome map based on sequencing mono- and dinucleosomal DNA fragments. The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species. We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes. We also describe a unique pattern found in the nucleosome-depleted region upstream of the TSS observed in the dinucleosome map and the precursor status of dinucleosomes prior to the digestion into mononucleosomes by comparing the mono- and dinucleosome maps. We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

RSOB120043F6: Profiles of the midpoints of highly positioned dinucleosomes of Mixia osmundae around the transcription start sites. The position profile of midpoints of highly positioned dinucleosomes in the vicinity of the TSS is compared between the three groups of genes showing distinct levels of expression. The nucleosomal midpoints of five or more piles were used.

Mentions:
The midpoint of a mononucleosome corresponds to the centre of the nucleosome core, whereas the midpoint of a dinucleosome lies in the linker DNA region flanked by two nucleosomes. Therefore, the peaks and bottoms of the midpoint profile of the mononucleosomes (figure 5) coincide, respectively, with the bottoms and peaks of the midpoint profile of dinucleosomes (figure 6). On the other hand, the interval between neighbouring peaks in the midpoint profile of dinucleosomes (figure 6) was identical to that of mononucleosomes (figure 5), indicating that the dinucleosomal DNA fragments were generated at random by MNase digestion. This result supports that MNase-digested dinucleosomes are precursors of mononucleosomes [40].Figure 5.

RSOB120043F6: Profiles of the midpoints of highly positioned dinucleosomes of Mixia osmundae around the transcription start sites. The position profile of midpoints of highly positioned dinucleosomes in the vicinity of the TSS is compared between the three groups of genes showing distinct levels of expression. The nucleosomal midpoints of five or more piles were used.

Mentions:
The midpoint of a mononucleosome corresponds to the centre of the nucleosome core, whereas the midpoint of a dinucleosome lies in the linker DNA region flanked by two nucleosomes. Therefore, the peaks and bottoms of the midpoint profile of the mononucleosomes (figure 5) coincide, respectively, with the bottoms and peaks of the midpoint profile of dinucleosomes (figure 6). On the other hand, the interval between neighbouring peaks in the midpoint profile of dinucleosomes (figure 6) was identical to that of mononucleosomes (figure 5), indicating that the dinucleosomal DNA fragments were generated at random by MNase digestion. This result supports that MNase-digested dinucleosomes are precursors of mononucleosomes [40].Figure 5.

Bottom Line:
The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species.We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes.We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

Affiliation:
Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan. hnishida@iu.a.u-tokyo.ac.jp

ABSTRACTWe present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nucleosome map based on sequencing mono- and dinucleosomal DNA fragments. The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species. We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes. We also describe a unique pattern found in the nucleosome-depleted region upstream of the TSS observed in the dinucleosome map and the precursor status of dinucleosomes prior to the digestion into mononucleosomes by comparing the mono- and dinucleosome maps. We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.